installing Tophat in fedora 17

[Rhizosis]

thanks a lot for ur valuable suggestions.,
i have entered as a root user so can i access the boost libraries.,

Be careful running applications as a root user. It is good practice to run all applications as a normal (non-sudo / non-root) user.

Else make the library files available in a different directory (a non root directory).

[Rhizosis]

And you should restart your shell if you have entered it in .bashrc file.
It wont recognise the export path before you have restarted the shell.

If you want to keep your shell open, just enter the export command in the shell.

Also, keep in mind that you should export the variable as the same user as you are running Tophat with.

[sudheer.svss]

That depends. Look at your path, is the boost library owned by root? If thats the case, try changing the ownership to the same user as you are running Tophat with. If Tophat cannot access the boost libraries because of user permissions you will get the same error.

thanks a lot for ur valuable suggestions.,
i have entered as a root user so can i access the boost libraries.,

[Rhizosis]

That depends. Look at your path, is the boost library owned by root? If thats the case, try changing the ownership to the same user as you are running Tophat with. If Tophat cannot access the boost libraries because of user permissions you will get the same error.

[sudheer.svss]

Try exporting LD_LIBRARY_PATH with the directory path of boost' lib folder.

export LD_LIBRARY_PATH=/folder/to/boost/dist/lib

and then run again.

thank you,
i have opened the vi .bash profile and added - export LD_LIBRARY_PATH=/root/NGS/boost_1_40_0/to/boost/dist/lib
as i have saved my boost 1.40 in a directory called NGS., is this the correct way to give the path.,
and i ran the test data but the same error is repeating.,

[Rhizosis]

Try exporting LD_LIBRARY_PATH with the directory path of boost' lib folder.

export LD_LIBRARY_PATH=/folder/to/boost/dist/lib

and then run again.

[sudheer.svss]

We are running the 64 bit version of tophat 2.0.6 with boost library 1.40 (2009).
This works perfectly. If all else fails, try the binary executable of Tophat 2.0.6 and argument the boost library path.

thank you,
i have installed boost 1.40 library., and i have removed all the boost 1.53 files in /usr/local/lib.,
now my /usr/local/lib contains only libbam.a
and i have installed boost 1.40 by sh configure.sh and after that ./bjam prefix =/usr/local link=static \ runtime-link=static stage install (as mentioned in the tophat getting started website).
and ran the tophat 2.0.6 by ./configure and make which showed

make all-recursive
make[1]: Entering directory `/root/NGS/tophat-2.0.6'
Making all in src
make[2]: Entering directory `/root/NGS/tophat-2.0.6/src'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/root/NGS/tophat-2.0.6/src'
make[2]: Entering directory `/root/NGS/tophat-2.0.6'
make[2]: Leaving directory `/root/NGS/tophat-2.0.6'
make[1]: Leaving directory `/root/NGS/tophat-2.0.6'


and make install - (i am mentioning the last few lines of the makeinstall running)
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/root/NGS/tophat-2.0.6/src'
make[1]: Leaving directory `/root/NGS/tophat-2.0.6/src'
make[1]: Entering directory `/root/NGS/tophat-2.0.6'
make[2]: Entering directory `/root/NGS/tophat-2.0.6'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/root/NGS/tophat-2.0.6'
make[1]: Leaving directory `/root/NGS/tophat-2.0.6'

then i have downloaded test data., and ran the command - tophat -r 20 test_ref reads_1.fq reads_2.fq which is showing error.,
[2013-02-12 21:45:09] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =127
/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.53.0: cannot open shared object file: No such file or directory
as I have removed these files from usr/local/lib and installed the boost 1.40., but still its mentioning the 1.53.0.,
please help me., as I am new to linux platform i am learning the basics of hte shell script., any guidance will help me a lot in this regard.,

[Rhizosis]

We are running the 64 bit version of tophat 2.0.6 with boost library 1.40 (2009).
This works perfectly. If all else fails, try the binary executable of Tophat 2.0.6 and argument the boost library path.

[sudheer.svss]

It looks like the boost library is not compatible with either your platform or with Tophat. Please check that again. Also make sure you have the latest g++ compiler installed.

hi, thankyou for ur suggestion., my linux fedora 17 platform is 64 bit x86, i have installed boost 1.53.0, and tophat version is 2.0.0.
first i have downloaded tophat-2.0.7.Linux_x86_64 and boost1.53 as mentioned in the tophat -getting started website., but i cudnt find ./configure file in that version of tophat., i spent a lot of time to resolve this but cudnt., so i downloaded tophat 2.0.0 version., and it has configure file and entered the make command which is showing the mentioned error., as i am trying with boost 1.48 version but cudnt resolve it., can u please provide further information.,

[Rhizosis]

It looks like the boost library is not compatible with either your platform or with Tophat. Please check that again. Also make sure you have the latest g++ compiler installed.

[sudheer.svss]

hi dears,
i am trying to install Tophat 2.0.0 in fedora 17. I have installed boost in usr/local/include. and downloaded samtools 0.1.18, copied libbam.a to usr/local/lib and .h files in to usr/local/include/bam.
I have copied the the executable files like bcftools, misc to usr/local/bin as mentioned., but I am not able to find samtools executables that are to be copied to usr/local/bin in the samtools 0.1.18.
i have run the make command in Tophat 2.0.0 and the error is

make all-recursive
make[1]: Entering directory `/root/NGS/tophat-2.0.0'
Making all in src
make[2]: Entering directory `/root/NGS/tophat-2.0.0/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -I./SeqAn-1.3 -o segment_juncs -L/usr/local/lib -L/usr/local/lib segment_juncs.o ../src/libtophat.a -lboost_thread -lbam -lz -lz
/usr/bin/ld: segment_juncs.o: undefined reference to symbol '_ZN5boost6system15system_categoryEv'
/usr/bin/ld: note: '_ZN5boost6system15system_categoryEv' is defined in DSO /usr/local/lib/libboost_system.so.1.53.0 so try adding it to the linker command line
/usr/local/lib/libboost_system.so.1.53.0: could not read symbols: Invalid operation
collect2: error: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/root/NGS/tophat-2.0.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/root/NGS/tophat-2.0.0'
make: *** [all] Error 2

please help me in this regard., as I am new to these installation steps I am not figureout the cause of error.